org.proteios.io.mzdata
Class MzDataExpSourceBlock

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation
              org.proteios.io.mzdata.MzDataExpCommonPeakListSet
                  org.proteios.io.mzdata.MzDataExpSourceBlock

public class MzDataExpSourceBlock
extends MzDataExpCommonPeakListSet

This class processes a "source" XML block in an mzData file. This class supports export of mzData files from Proteios. An mzData file contains information on a mass spectrometry experiment. Given a Proteios peakListSet, MzDataExporter fetches stored data related to this peakListSet and stores it in an mzData file.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-10-25 14:40:28 +0200 (Wed, 25 Oct 2006) $

Field Summary

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

anna, dc, factory

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommon

log

Constructor Summary

MzDataExpSourceBlock(SessionControl sc)
Default constructor.

Method Summary

void	fetchPeakListSetAnnotations(PeakListSet peakListSet, DbControl dc) Fetches variable values stored as annotations for ionisationSource.
void	write(XMLCrudeWriter xmlCrudeWriter, PeakListSet peakListSet) Creates a source block.

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonPeakListSet

getPeakListSet, setPeakListSet

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonAnnotation

createAddedParamAnnotationType, createAnnotationType, createCvLookupAnnotationType, createCvParamAnnotationType, createUserParamAnnotationType, fetchAddedParamAnnotationType, fetchAnnotation, fetchCvLookupAnnotation, fetchCvLookupAnnotationList, fetchCvLookupAnnotationType, fetchCvParamAnnotation, fetchCvParamAnnotationList, fetchUserParamAnnotation, fetchUserParamAnnotationList, obtainAddedParamAnnotationType, obtainCvLookupAnnotationType, storeAnnotation, storeCvLookupAnnotation, storeCvParamAnnotation, storeUserParamAnnotation

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

enableAnnotator, enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommon

getBlockTagName, setBlockTagName, write, writeAttribute, writeEndTag, writeNamespace, writeSimpleElementPair, writeSimpleElementPair, writeSingleElementEnd, writeStartElement, writeStartElementEnd, writeStartListTag, writeStartTag, zeroPad, zeroPad, zeroPad

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MzDataExpSourceBlock

public MzDataExpSourceBlock(SessionControl sc)

Default constructor.

Parameters:

sc -

Method Detail

write

public void write(XMLCrudeWriter xmlCrudeWriter,
                  PeakListSet peakListSet)
           throws javax.xml.stream.XMLStreamException

Creates a source block.

Parameters:

xmlCrudeWriter - the XMLCrudeWriter instance to use.

peakListSet - PeakListSet peakListSet used

Throws:

javax.xml.stream.XMLStreamException - If there is an XML Stream related error

fetchPeakListSetAnnotations

public void fetchPeakListSetAnnotations(PeakListSet peakListSet,
                                        DbControl dc)

Fetches variable values stored as annotations for ionisationSource.

Parameters:

peakListSet - PeakListSet peakListSet used to retrieve data